The eukaryotic SMC (structural maintenance of chromosomes) proteins and associated subunits form two types of complexes in eukaryotic organisms, including budding yeast. These protein complexes, termed cohesin and condensin, largely determine chromosome structure in mitotically dividing cells. Condensin localisation and high-resolution ChIP analysis revealed that the rDNA locus is the primary target of condensin activity in vivo. We undertook genetic and cytological screens for the factors required for mitosis-specific binding of condensin to chromatin. We identified a range of cis?factors responsible for mitosis-specific condensin targeting to rDNA chromatin. Among them were cell-cycle regulators and chromatin proteins. Alanine-scanning mutagenesis of Mcd1p, a subunit of mitotic cohesin, identified domains responsible for establishment and dissolution of sister chromatid cohesion. The S. cerevisiae mitotic cohesin complex was reconstituted from recombinant subunits. We also reconstituted the hypothetical meiotic cohesin. Analysis of somatic pairing between yeast chromosomes in live cells led to the discovery of interchromosome transassociations, a DNA-homology-dependent mechanism, mediating transient but reproducible interaction between ectopic chromosomal sites in the genome.